# ========= [INFO] ==========
# Mut inCB: not accepter mutation in BC
# Mut inMS: 2
# ReadIn  : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam
# seq_deb : GTCAGTG
# seq_fin : CGTGG
# MS_seq : AT
# excl : C,G
# nom  : AT25
# =============================
#
#-------------- Filt ------------------
# condiGrep: GTCA.TG[ATCGN]+ATATATATAT[ATCGN]+.GTGG|GTCA.TG[ATCGN]+ATATATATAT[ATCGN]+C.TGG|GTCA.TG[ATCGN]+ATATATATAT[ATCGN]+CG.GG|GTCA.TG[ATCGN]+ATATATATAT[ATCGN]+CGT.G|GTCA.TG[ATCGN]+ATATATATAT[ATCGN]+CGTG.|GTCAG.G[ATCGN]+ATATATATAT[ATCGN]+.GTGG|GTCAG.G[ATCGN]+ATATATATAT[ATCGN]+C.TGG|GTCAG.G[ATCGN]+ATATATATAT[ATCGN]+CG.GG|GTCAG.G[ATCGN]+ATATATATAT[ATCGN]+CGT.G|GTCAG.G[ATCGN]+ATATATATAT[ATCGN]+CGTG.|GTCAGT.[ATCGN]+ATATATATAT[ATCGN]+.GTGG|GTCAGT.[ATCGN]+ATATATATAT[ATCGN]+C.TGG|GTCAGT.[ATCGN]+ATATATATAT[ATCGN]+CG.GG|GTCAGT.[ATCGN]+ATATATATAT[ATCGN]+CGT.G|GTCAGT.[ATCGN]+ATATATATAT[ATCGN]+CGTG.
# condiGrep Rev-Compt: .CACG[NCGAT]+ATATATATAT[NCGAT]+.ACTGAC|C.ACG[NCGAT]+ATATATATAT[NCGAT]+.ACTGAC|CC.CG[NCGAT]+ATATATATAT[NCGAT]+.ACTGAC|CCA.G[NCGAT]+ATATATATAT[NCGAT]+.ACTGAC|CCAC.[NCGAT]+ATATATATAT[NCGAT]+.ACTGAC|.CACG[NCGAT]+ATATATATAT[NCGAT]+C.CTGAC|C.ACG[NCGAT]+ATATATATAT[NCGAT]+C.CTGAC|CC.CG[NCGAT]+ATATATATAT[NCGAT]+C.CTGAC|CCA.G[NCGAT]+ATATATATAT[NCGAT]+C.CTGAC|CCAC.[NCGAT]+ATATATATAT[NCGAT]+C.CTGAC|.CACG[NCGAT]+ATATATATAT[NCGAT]+CA.TGAC|C.ACG[NCGAT]+ATATATATAT[NCGAT]+CA.TGAC|CC.CG[NCGAT]+ATATATATAT[NCGAT]+CA.TGAC|CCA.G[NCGAT]+ATATATATAT[NCGAT]+CA.TGAC|CCAC.[NCGAT]+ATATATATAT[NCGAT]+CA.TGAC
#--------------------------------------
module load picard/2.8.2
> java -jar /env/gfs/apps/picard/2.8.2/picard.jar SortSam I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.unmapped.sam O=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.unmapped.sort.sam SORT_ORDER=queryname 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.unmapped.bam ]
